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- PDB-1cr7: PEANUT LECTIN-LACTOSE COMPLEX MONOCLINIC FORM -

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Basic information

Entry
Database: PDB / ID: 1cr7
TitlePEANUT LECTIN-LACTOSE COMPLEX MONOCLINIC FORM
ComponentsLECTIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / MONOCLINIC FORM / ACIDIC PH / LACTOSE
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-lactose / : / : / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRavishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
Citation
Journal: Proteins / Year: 2001
Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal ...Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.
Authors: Ravishankar, R. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N- Acetyllactosamine and a Comparative Study of Carbohydrate Binding in Gal/ Galnac-Specific Legume Lectins
Authors: Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
#2: Journal: Curr.Sci. / Year: 1997
Title: The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges
Authors: Ravishankar, R. / Ravindran, M. / Suguna, K. / Surolia, A. / Vijayan, M.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Conformation, Protein-Carbohydrate Interactions and a Novel Subunit Association in the Refined Structure of Peanut Lectin-Lactose Complex
Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of Peanut Lectin, a Protein with an Unusual Quaternary Structure
Authors: Banerjee, R. / Mande, S.C. / Ganesh, V. / Das, K. / Dhanaraj, V. / Mahanta, S.K. / Suguna, K. / Surolia, A. / Vijayan, M.
History
DepositionAug 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,45927
Polymers201,6728
Non-polymers1,78719
Water12,665703
1
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90014
Polymers100,8364
Non-polymers1,06510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55813
Polymers100,8364
Non-polymers7229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.320, 126.820, 85.610
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsTHERE ARE TWO TETRAMERS IN THE ASYMMETRIC UNIT WITHOUT 222 OR FOUR-FOLD SYMMETRY. CHAINS A,B,C AND D FORM ONE TETRAMER WHILE CHAINS E,F,G AND H FORM THE OTHER INDEPENDENT TETRAMER

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Components

#1: Protein
LECTIN / AGGLUTININ


Mass: 25208.955 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: PIR: S14765, UniProt: P02872*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 4.6
Details: PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M ...Details: PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M SODIUM ACETATE BUFFER CONTAINING 0.2 M SODIUM CHLORIDE, 1.5 MM LACTOSE AND 0.05 %SODIUM AZIDE. THE PRECIPITANT USED WAS PEG 8000, A SOLUTION OF WHICH IN THE SAME BUFFER WAS ADDED TO A FINAL CONCENTRATION OF ABOUT 12%. THE TUBES WERE LEFT UNDISTURBED FOR ABOUT TWO WEEKS, BY WHICH TIME CRYSTALS SUITABLE FOR DATA COLLECTION GREW., SMALL TUBES, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: microdialysis / Details: Salunke, D.M., (1983) FEBS Lett., 156, 127.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
340 %(w/v)PEG60001drop
40.2 M1reservoirNaCl
50.05 Msodium acetate1reservoir
61.5 mMlactose1reservoir
2phosphate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 65505 / % possible obs: 86.3 % / Redundancy: 4.75 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.134
Reflection
*PLUS
Num. measured all: 311508
Reflection shell
*PLUS
% possible obs: 68.4 % / Rmerge(I) obs: 0.316

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PEL

2pel


Resolution: 2.6→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. NCS CONSTRAINTS WERE APPLIED WITHIN EACH OF THE FOLLOWING GROUPS: SUBUNITS A, B, E; SUBUNITS C, G; SUBUNITS D, H
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1168 2 %RANDOM
Rwork0.207 ---
obs0.212 58584 78.9 %-
Solvent computationSolvent model: BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 85 703 14732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.671.5
X-RAY DIFFRACTIONx_mcangle_it10.522
X-RAY DIFFRACTIONx_scbond_it4.062
X-RAY DIFFRACTIONx_scangle_it5.722.5
Refine LS restraints NCSNCS model details: RESTRAIN
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 175 2.3 %
Rwork0.289 7337 -
obs--60.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARWAT.TOP
X-RAY DIFFRACTION3PARAM1.CHOTOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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